bioinformatics

Mentors and Regional Facilitators

Name	Region	Skills	Interests
Brett Milash	RMACC	bioinformatics python
Carrie Brown	CAREERS, ACCESS CSSN	bioinformatics cleanup community-outreach data-wrangling distributed-computing genomics github github-pages more...
Balamurugan Desinghu	ACCESS CSSN, Campus Champions, CAREERS, Northeast	ai anaconda api bash batch-jobs benchmarking big-data bioinformatics more...	affinity-group ai allocations-proposal amber anaconda archiving backup bash more...
Diana Toups Dugas	RMACC, SWEETER, Campus Champions	bioinformatics biology genomics proposal-development research-facilitation software-carpentry training workforce-development
Jordan Hayes	Campus Champions	acls administering-hpc amber anaconda api atlas aws bash more...
Jacob Pessin	Northeast	aws bash batch-jobs big-data bioinformatics cloud-storage cluster-support cyverse more...
Juan Vanegas	Northeast	bash batch-jobs bioinformatics compiling conda environment-modules hpc-cluster-build hpc-operations more...
Larry Feinstein	Northeast	bioinformatics
shuai liu	ACCESS CSSN	ai anaconda azure big-data bioinformatics biology containers data-analysis more...
Nick Dusek	Campus Champions	administering-hpc anaconda bash batch-jobs bioinformatics compiling containers data-transfer more...
Nect Admin	Great Plains, Northeast, RMACC	astrophysics bioinformatics cgroups data-lifecycle deep-learning file-transfer	science-gateway
Nicholas Panchy	Campus Champions	bash bioinformatics biology conda easybuild genomics modules ondemand more...
Rob Harbert	Northeast	anaconda batch-jobs big-data bioinformatics biology distributed-computing genomics gis more...
Shane Sanders	Campus Champions	bioinformatics c c++ containers machine-learning programming python research-grants more...	archiving big-data data-analysis data-compliance data-lifecycle data-management data-reproducibility data-retention more...
Xiaoqin Huang	ACCESS CSSN	access-account ACCESS-credits adding-users affinity-group allocations-extension allocations-proposal amber anaconda more...	ACCESS-credits ACCESS-website adding-users affinity-group allocations-extension allocations-proposal amber anaconda more...
William Sanders	Campus Champions	bioinformatics c c++ containers machine-learning programming python research-grants more...	archiving big-data data-analysis data-compliance data-lifecycle data-management data-reproducibility data-retention more...
William Lai	ACCESS CSSN	administering-hpc ai anaconda archiving backup bash bioinformatics biology more...	administering-hpc ai archiving bash benchmarking big-data bioinformatics biology more...
Ying Zhang	CAREERS	bioinformatics	bioinformatics deep-learning
Yun Shen	CAREERS, Northeast, ACCESS CSSN	big-data bioinformatics data-analysis data-science genomics ondemand programming Programming more...

Users

Name	Roles	Skills	Interests
Aidan McCrillis	student facilitator	bioinformatics biology data-science python
Carrie Brown	mentor steering committee	bioinformatics cleanup community-outreach data-wrangling distributed-computing genomics github github-pages more...
Balamurugan Desinghu	mentor researcher/educator rcf	ai anaconda api bash batch-jobs benchmarking big-data bioinformatics more...	affinity-group ai allocations-proposal amber anaconda archiving backup bash more...
Emma Strand	student facilitator	anaconda archiving bash big-data bioinformatics biology community-outreach data-analysis more...
Eren Ada	student facilitator	anaconda bash big-data bioinformatics biology community-outreach compiling dependencies more...
Chris Hemme	researcher/educator	anaconda big-data bioinformatics biology data-analysis genomics r	anaconda big-data bioinformatics biology data-analysis genomics python r
Hening Cui	student facilitator	bioinformatics biology cleanup data-analysis java machine-learning natural-language-processing neural-networks more...
Ifeoma Ugwuanyi	student facilitator	bioinformatics biology data-analysis genomics python r sql	anaconda big-data bioinformatics biology data-analysis data-wrangling genomics python more...
Kenneth Acosta	student facilitator	bash bioinformatics biology conda genomics github pip python more...	batch-jobs cluster-management cluster-support data-management data-transfer distributed-computing programming-best-practices scheduling
Vinayak Mathur	researcher/educator	bioinformatics biology genomics
Lenore Martin	researcher/educator	administering-hpc amber anaconda backup bash bioinformatics biology charmm more...	administering-hpc ai amber anaconda bioinformatics biology charmm community-outreach more...
Xiaoluo Jiao	student facilitator	bioinformatics biology cleanup data-management data-reproducibility data-wrangling genomics git more...	python sql
Sanguthevar Ra…	researcher/educator	ai big-data bioinformatics biology computational-chemistry data-analysis data-science deep-learning more...
William Feng	student facilitator	bioinformatics biology data-analysis genomics java programming programming-best-practices python more...
Ying Zhang	mentor researcher/educator	bioinformatics	bioinformatics deep-learning
Yun Shen	mentor	big-data bioinformatics data-analysis data-science genomics ondemand programming Programming more...

Projects

Project Title	Project Institution Sort descending	Project Owner	Tags	Status
High throughput Python pipeline to identify Horizontal Gene Transfer	Cabrini University	Vinayak Mathur	bioinformatics, biology, data-wrangling, genomics, github, python, workflow	Halted
Parallel analysis of variants in multiple bear genomes: algorithmic solutions	Rutgers University–Camden	Galen Collier	Data-Facing, bioinformatics	Complete
Metagenomic analysis to identify gene clusters associated with IgA production	SUNY Upstate Medical University	Joel Wilmore	bioinformatics, biology, genomics, python, r, research-facilitation	Finishing Up
Deep convolutional neural networks (dCNN) for image segmentation, instance labeling, and tracking.	University of Delaware	Anita Schwartz	bash, bioinformatics, computational-chemistry, debugging, machine-learning, programming, python, scripting, slurm, software-installation, tensorflow	Complete
Novel Transformer based methods for Automatic Classification and Quantification of Stromule Dynamics from Microscopy Images	University of Delaware	Anita Schwartz	bioinformatics	Complete
Assembly and Taxonomic Profiling of Metagenomic Sequences using Deep Learning	University of Rhode Island	Gaurav Khanna	ai, bioinformatics, biology, deep-learning, gpu, hardware, machine-learning, neural-networks, python	Complete
Computational pipelines for the analysis of plastic-degrading genes	University of Rhode Island	Gaurav Khanna	bioinformatics, biology, workflow, workforce-development	In Progress
Host-symbiont population genomics - analyzing the intraspecific variability of methanogenic archaeal endosymbionts of genus Methanocorpusculum hosted by a marine anaerobic ciliate Metopus sp. (Metopida)	University of Rhode Island -- Bay Campus	Gaurav Khanna	bioinformatics, biology, genomics	Complete
Develop a data portal for the organization of molecular and imaging data	University of Rhode Island -- Bay Campus	Gaurav Khanna	archiving, aws, bioinformatics, biology, Cloud, Data Storage, docker, genomics	In Progress

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Affinity Groups

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Announcements

Title	Date
Ookami Webinar	02/14/24
2024 HuBMAP Underrepresented Student Internship Program	10/31/23
Open Call: Minisymposia for PASC24	10/05/23

Upcoming Events & Trainings

No events or trainings are currently scheduled.

Topics from Ask.CI

Resources

Title	Category	Tags	Skill Level
Optimizing Research Workflows - A Documentation of Snakemake	Docs	documentation, data-analysis, data-reproducibility, workflow, bioinformatics, data-science, python	Intermediate, Advanced
Samtools Documentation	Docs	documentation, data-analysis, bioinformatics, data-science, genomics	Beginner, Intermediate, Advanced
Bioinformatics Workflow Management with Nextflow	Docs	cloud-computing, parallelization, data-management, bioinformatics, training	Beginner, Intermediate

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People with Expertise

Ying Zhang

University of Rhode Island

Programs

CAREERS

Roles

mentor, researcher/educator

Expertise

Nect Admin

Worcester Polytechnic Institute

Programs

Great Plains, Northeast, RMACC

Roles

administrator, ci systems engineer

Expertise

astrophysics

cgroups

deep-learning

+1 more tags

Audrey Law

Bluegrass Community and Technical College

Programs

Kentucky

Roles

researcher/educator

Expertise

data-analysis

genomics

git

github

+1 more tags

People with Interest

yaniv kovalski

Stonehill College

Programs

Northeast

Roles

student-facilitator

Interests

ai

big-data

bioinformatics

cluster-management

data-analysis

+4 more tags

Xilin Qiao

Programs

ACCESS CSSN

Roles

student-facilitator

Interests

access-website

ai

api

aws

azure

+27 more tags

diana Trotman

Queens borough community college

Programs

CAREERS

Roles

student-facilitator, research computing facilitator, mentee

Student facilitator

Interests

benchmarking

bioinformatics

biology

cleanup

cloud-commercial

+29 more tags